The church hall in central London was standing-room only, the atmosphere charged. In a room draped in banners carrying the slogan "Workers' Rights are Human Rights", a union rep summed up the mood: "We are here and we are pissed off." These were not the disgruntled workers of a large corporation, but the staff of Amnesty International, their anger not focused on human rights abuse, but on their own management.

The battle between Amnesty staff and management has intensified in recent months following proposals to restructure the organisation. Strikes have been held at both the UK branch and the international secretariat headquarters in London and picket lines have formed in solidarity outside offices around the world. Staff have given management a vote of no confidence and – in response to more than 100 members expressing concern about changes taking place in the organisation – an extraordinary general meeting has been called for January.

The core of the dispute lies in the decision, led by the secretary general, Salil Shetty, to take the organisation "closer to the ground", opening 10 new regional "hubs" in hotspots where human rights violations occur. Some of Amnesty's 500 staff in London will be moved abroad, and those affected argue that the shift is under-planned, ill-judged and risks muddying the purpose of the organisation. For them this is not an industrial dispute over job cuts, but a battle for the organisation's soul.

According to Thomas Schultz-Jagow, Amnesty's senior director of campaigns and communications, the organisation has no choice but to adapt to a changing world. "It is anachronistic to have an organisation with more than 500 people in London when we need to be where these abuses are happening, we need to be where the action is," he said. "If we do nothing, we will lose influence and become out of touch with those places where human rights violations are happening."

The majority of workers the Guardian spoke to agreed, in principle, with the proposal. So how have relations become so bitter? Schultz-Jagow said that although the proposals had been on the table for two years, only now were cuts to staff being implemented and he suggested Unite, the workers' union, was stalling the process.

"The role of Unite is to keep as many jobs in London as possible, and our job is to deliver a global strategy," he said. "We have huge sympathy for the people who are impacted but we also have a responsibility to take this forward."

The complaints at Amnesty's two offices in London vary. Workers in the UK section fear the security risks in opening new offices in often dangerous places have not been properly assessed, that human rights work and impartiality could be put at risk and that AI UK could, in the words of one worker, be turned into a "cash cow" rather than a campaigning hub. In the UK section, 23 posts will be made redundant, reducing the total from 171 to 148; the number set to go in the international secretariat has yet to be established.

Workers are incensed that redundancy terms have been torn up before cuts are made, with three weeks' payments given for every year of service rather than four. By contrast, Shetty's predecessor, Irene Khan, received £530,000 – four times her salary – on leaving Amnesty last year. Her deputy, Kate Gilmore, who left at the same time as Khan, was paid £320,000.

Three programme directors have left in the last year. The most recent, Susan Lee, the Americas programme director, resigned last month because of "senior management's failure to honour its commitments to treat staff fairly and with respect". The next day, the union voted to strike, saying it had lost all confidence in management because it lacked "integrity, competence, transparency and accountability".

It is, according to one worker in the AI UK office, a "stressful and unhappy" time. "In my most fearful moment I feel we are on a precipice, that we are unintentionally and thoughtlessly putting the future of the movement at risk," said the worker, who did not want to be named. "I worry that we could be seeing the unravelling of an inspiring idea that has been hugely successful."

Amnesty was formed in 1961 after a British lawyer, Peter Benenson, on hearing that two Portuguese students had been imprisoned for drinking a toast to liberty, wrote an article in the Observer suggesting prisoners of conscience might be released if people wrote letters to governments.

Since then its scope has become much more far-reaching, encompassing support for abortion rights, the right to a fair trial and opposition to the death penalty. Shetty, who took up the role two years ago, has gone further – positioning the organisation as a champion of economic, cultural and social rights – with the argument that "the ultimate torture is poverty".

Critics argue Amnesty has lost its focus and too much emphasis has been put on the brand rather than human rights work. As one worker put it: "There is a fear that the hubs are more about media and communications than about campaigning for human rights. Are we there to publicise Amnesty, or fight for those rights?"

Kate Allen, head of AI UK, insisted that the difficult changes happening in the organisation were vital for that fight to continue. "We have to have members all over the world, we have to have workers on the ground lobbying governments," she said. "You can't have that influence just by flying in. You need to be there." Redundancies were "really tough", she said, but despite calls for her resignation she believes she can lead the section through the changes. "It was quite horrible to hear my resignation called for," she said. "But I absolutely stand by this decision. I don't want to think about what Amnesty International would be like in 10 years' time if it didn't happen."

The picture may be bleak for workers in the UK, but new offices are brimming with enthusiasm. Atila Roque, director of the newly opened Brazil office, said his team of six, which is expected to grow to about 30, was already making inroads with local groups and governments. It does not yet count its members in Brazil but aims to enlist 30-40,000 activists in the next three to five years. "It's a huge challenge, but to be a global human rights organisation, to be a legitimate actor, we need to be here on the ground," he said.

The battle in the UK appears to have reached an impasse, but Allen hopes the extraordinary general meeting will clear the air. "We are having a fierce debate, but we will come through it," she said. "It doesn't feel like [Amnesty] is broken; it feels like we are having a hard time changing but we will achieve it." One of her workers agreed, but only in part. "It is not a bad thing to have a look and think about what we do," she said. "As long as we don't tear ourselves apart in the process."

Update: 20 December. We have been asked to make clear that the figure paid to Irene Khan on termination of her employment included numerous entitlements most of which were her salary and benefits earned over several years in the course of her employment, rather than being a sum in respect of her termination.